org.jmol.adapter.smarter
Class Atom

java.lang.Object
  extended by javax.vecmath.Tuple3f
      extended by javax.vecmath.Point3f
          extended by org.jmol.adapter.smarter.Atom
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class Atom
extends javax.vecmath.Point3f
implements java.lang.Cloneable

See Also:
Serialized Form

Field Summary
 char alternateLocationID
           
 float[] anisoBorU
           
 int atomIndex
           
 java.lang.String atomName
           
 int atomSerial
           
 int atomSetIndex
           
 int atomSite
           
 float bfactor
           
 java.util.BitSet bsSymmetry
           
 char chainID
           
(package private) static int[] elementCharMasks
          Bits which indicate whether or not an element symbol is valid.
 short elementNumber
           
 java.lang.String elementSymbol
           
 java.lang.Object[] ellipsoid
           
 int formalCharge
           
 java.lang.String group3
           
 char insertionCode
           
 boolean isHetero
           
 int occupancy
           
 float partialCharge
           
 float radius
           
 int sequenceNumber
           
 float vectorX
           
 float vectorY
           
 float vectorZ
           
 
Fields inherited from class javax.vecmath.Tuple3f
x, y, z
 
Constructor Summary
Atom()
           
 
Method Summary
 void addVibrationVector(float vectorX, float vectorY, float vectorZ)
           
 Atom cloneAtom()
           
 java.lang.String getElementSymbol()
           
static boolean isValidElementSymbol(char ch)
           
static boolean isValidElementSymbol(char chFirst, char chSecond)
           
static boolean isValidElementSymbolNoCaseSecondChar(char chFirst, char chSecond)
           
static boolean isValidElementSymbolNoCaseSecondChar(java.lang.String str)
           
static boolean isValidFirstSymbolChar(char ch)
           
 
Methods inherited from class javax.vecmath.Point3f
distance, distanceL1, distanceLinf, distanceSquared, project
 
Methods inherited from class javax.vecmath.Tuple3f
absolute, absolute, add, add, clamp, clamp, clampMax, clampMax, clampMin, clampMin, epsilonEquals, equals, get, get, hashCode, interpolate, interpolate, negate, negate, scale, scale, scaleAdd, scaleAdd, set, set, set, set, sub, sub, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

atomSetIndex

public int atomSetIndex

atomIndex

public int atomIndex

bsSymmetry

public java.util.BitSet bsSymmetry

atomSite

public int atomSite

elementSymbol

public java.lang.String elementSymbol

elementNumber

public short elementNumber

atomName

public java.lang.String atomName

formalCharge

public int formalCharge

partialCharge

public float partialCharge

vectorX

public float vectorX

vectorY

public float vectorY

vectorZ

public float vectorZ

bfactor

public float bfactor

occupancy

public int occupancy

radius

public float radius

isHetero

public boolean isHetero

atomSerial

public int atomSerial

chainID

public char chainID

alternateLocationID

public char alternateLocationID

group3

public java.lang.String group3

sequenceNumber

public int sequenceNumber

insertionCode

public char insertionCode

anisoBorU

public float[] anisoBorU

ellipsoid

public java.lang.Object[] ellipsoid

elementCharMasks

static final int[] elementCharMasks
Bits which indicate whether or not an element symbol is valid.

If the high bit is set, then it is valid as a standalone char. otherwise, bits 0-25 say whether or not is valid when followed by the letters a-z.

Constructor Detail

Atom

public Atom()
Method Detail

cloneAtom

public Atom cloneAtom()
               throws java.lang.Exception
Throws:
java.lang.Exception

getElementSymbol

public java.lang.String getElementSymbol()

addVibrationVector

public void addVibrationVector(float vectorX,
                               float vectorY,
                               float vectorZ)

isValidElementSymbol

public static boolean isValidElementSymbol(char ch)

isValidElementSymbol

public static boolean isValidElementSymbol(char chFirst,
                                           char chSecond)

isValidElementSymbolNoCaseSecondChar

public static boolean isValidElementSymbolNoCaseSecondChar(char chFirst,
                                                           char chSecond)

isValidFirstSymbolChar

public static boolean isValidFirstSymbolChar(char ch)

isValidElementSymbolNoCaseSecondChar

public static boolean isValidElementSymbolNoCaseSecondChar(java.lang.String str)